10-93926824-C-G

Variant names:

• chr10-93926824-C-G
• rs829237
• ENST00000605679.5:n.*253+14025C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000605679.5(SLC35G1):​n.*253+14025C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,998 control chromosomes in the GnomAD database, including 18,481 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18481 hom., cov: 32)
• Consequence: SLC35G1 ENST00000605679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900

Genes affected

SLC35G1 (HGNC:26607): (solute carrier family 35 member G1) This gene encodes a transmembrane protein which is a member of the drug/metabolite transporter protein superfamily. The encoded protein may play a role in the regulation of calcium levels inside the cell. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35G1	ENST00000605679.5	n.*253+14025C>G		intron_variant	Intron 3 of 3	1		ENSP00000474890.1
SLC35G1	ENST00000494992.5	n.*253+14025C>G		intron_variant	Intron 3 of 4	5		ENSP00000474294.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73423 AN: 151880 Hom.: 18472 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.448

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.483 AC: 73474 AN: 151998 Hom.: 18481 Cov.: 32 AF XY: 0.490 AC XY: 36378 AN XY: 74288

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.449

Alfa AF: 0.460 Hom.: 1978

Bravo AF: 0.481

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs829237; hg19: chr10-95686581;